Taking variation of evolutionary rates between sites into account in inferring phylogenies

Journal of Molecular Evolution

Volumn 53, Issue 4-5, 2001, Pages 447-455

  Felsenstein, Joseph ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Distance; Evolutionary rate; Invariants; Maximum likelihood; Parsimony; Phylogeny

Indexed keywords

RNA;

ARTICLE; GENETIC DISORDER; MAXIMUM LIKELIHOOD METHOD; MOLECULAR EVOLUTION; PHYLOGENY; RNA SEQUENCE; STATISTICAL MODEL;

ALGORITHMS; EVOLUTION, MOLECULAR; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; MUTATION; PHYLOGENY; TIME FACTORS;

EID: 0034818755     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002390010234     Document Type: Article

References (33)

1. Molecular evolution modeled as a fractal poisson process in agreement with mammalian sequence comparisons
2. Invariants of phylogenies in a simple case with discrete states
3. Estimating divergence times in the presence of an overdispersed molecular clock
4. A successive approximations approach to character weighting
5. Evolutionary trees from DNA sequences: A maximum likelihood approach
6. A likelihood approach to character weighting and what it tells us about parsimony and compatibility
7. A hidden Markov model approach to variation among sites in rate of evolution
8. Self-weighted optimization: Tree searches and character state reconstructions under implied transformation costs
9. Dating of the human-ape splitting by a molecular clock of mitchondrial DNA
10. Success of phylogenetic methods in the 4-taxon case
11. A compound poisson process for relaxing the molecular clock
12. Limitations of the evolutionary parsimony method of phylogenetic analysis
13. Evolution of protein molecules
14. Some problems of stochastic processes in genetics
15. On the probability of fixation of mutant genes in a population
16. A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
17. A rate-independent technique for analysis of nucleic acid sequences: Evolutionary parsimony
18. A new method for calculating evolutionary substitution rates
19. Infinite allele model with varying mutation rate
20. Molecular studies of evolution: A source of novel statistical problems
21. The current significance and standing of neutral and nearly neutral theories
22. Earliest phylogenetic branchings: Comparing rRNA-based evolutionary trees inferred with various techniques
23. Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences
24. A nonparametric approach to estimating divergence times in the absence of rate constancy
25. Generation time and genomic evolution in primates
26. Estimating the rate of evolution of the rate of molecular evolution
27. General time-reversible distances with unequal rates across sites: Mixing gamma and inverse Gaussian distributions with invariant sites
28. Maximum-likelihood-estimation of phylogeny from DNA sequences when substitution rates differ over sites
29. Maximum-likelihood phylogenetic estimation from DNA sequences with variable rates over sites - Approximate methods
30. A space-time process model for the evolution of DNA sequences
31. Maximum-likelihood models for combined analyses of multiple sequence data